chr1-25618206-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020379.4(MAN1C1):c.409G>A(p.Glu137Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,590,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020379.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAN1C1 | NM_020379.4 | c.409G>A | p.Glu137Lys | missense_variant | 1/12 | ENST00000374332.9 | NP_065112.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN1C1 | ENST00000374332.9 | c.409G>A | p.Glu137Lys | missense_variant | 1/12 | 1 | NM_020379.4 | ENSP00000363452 | P1 | |
MAN1C1 | ENST00000263979.7 | c.-257G>A | 5_prime_UTR_variant | 1/13 | 5 | ENSP00000263979 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000147 AC: 3AN: 203650Hom.: 0 AF XY: 0.0000178 AC XY: 2AN XY: 112386
GnomAD4 exome AF: 0.0000174 AC: 25AN: 1438066Hom.: 0 Cov.: 31 AF XY: 0.0000154 AC XY: 11AN XY: 713962
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2024 | The c.409G>A (p.E137K) alteration is located in exon 1 (coding exon 1) of the MAN1C1 gene. This alteration results from a G to A substitution at nucleotide position 409, causing the glutamic acid (E) at amino acid position 137 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at